to modify a skill effects I (using ComputerSystemsEffect1 as an example)
- found ComputerSystemsEffect1.class file in SSP.jar in data\characters\skills\scripts\ folder (.jar opens like an archive by 7zip);
- decompiled this .class file in to readable form by using online decompiler (javadecompilers.com in my case);
- saved this decompiled contents as a plain text file, naming it ComputerSystemsEffect1.java;
- created \scripts folder in Starsector Plus\data\characters\skills folder;
- placed newly created ComputerSystemsEffect1.java therein;
- erased ComputerSystemsEffect1.java and ComputerSystemsEffect1.class files from SSP.jar, like you would do with a usual .rar or .zip;
- modified .java file to my heart's content, and happily played with modified numbers actually appearing in SS+!
P.S. works for aptitudes too